Fixes to code for remaining tests. TestModificationInfoListProteinGroupsOutput() was not consistent when run individually vs when run with all other tests. The ordering of the output was changing. Fixed to not look for the first data line but rather for the one with the right PG.

Author: pcruzparri

MetaMorpheus/EngineLayer/ProteinParsimony/ProteinGroup.cs

@@ -170,7 +170,7 @@ public string GetTabSeparatedHeader()
             sb.Append("Fragment Sequence Coverage" + '\t');
             //sb.Append("Modification Info List" + "\t");
 
-            if (FilesForQuantification != null)
+            if (IntensitiesByFile != null && FilesForQuantification != null)
             {
                 bool unfractionated = FilesForQuantification.Select(p => p.Fraction).Distinct().Count() == 1;
                 bool conditionsUndefined = FilesForQuantification.All(p => string.IsNullOrEmpty(p.Condition));
@@ -204,8 +204,12 @@ public string GetTabSeparatedHeader()
                     }
                 }
             }
+            else
+            {
+                sb.Append("\t");
+            }
 
-            sb.Append("Number of PSMs" + '\t');
+                sb.Append("Number of PSMs" + '\t');
             sb.Append("Protein Decoy/Contaminant/Target" + '\t');
             sb.Append("Protein Cumulative Target" + '\t');
             sb.Append("Protein Cumulative Decoy" + '\t');

MetaMorpheus/Test/ProteinGroupTest.cs

@@ -247,8 +247,10 @@ public static void TestModificationInfoListInProteinGroupsOutput()
             Assert.That(totalNumberOfMods, Is.EqualTo(4));
 
             List<string> proteinGroupsOutput = File.ReadAllLines(Path.Combine(outputFolder, "task2", "AllQuantifiedProteinGroups.tsv")).ToList();
-            string firstDataLine = proteinGroupsOutput[2];
-            string modInfoListProteinTwo = firstDataLine.Split('\t')[14];
+            string testDataLine = proteinGroupsOutput.Where(x => x.StartsWith("P10591")).First();
+            string modInfoListProteinTwo = testDataLine.Split('\t')[14];
+
+            Assert.That(8, Is.EqualTo(proteinGroupsOutput.Count));
             Assert.That(modInfoListProteinTwo, Is.EqualTo("P10591:{M#65[Common Variable:Oxidation on M, info: occupancy=1.0000(654315.977066199)]S#71[Less Common:Oxidation on S, info: occupancy=0.1957(654315.977066199)]}" +
                                                           "P10592:{M#65[Common Variable:Oxidation on M, info: occupancy=1.0000(654315.977066199)]S#71[Less Common:Oxidation on S, info: occupancy=0.1957(654315.977066199)]}"));